POInT browse : orthology prediction and synteny exploration for paleopolyploid genomes.

Autor: Siddiqui M; Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA., Conant GC; Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA. gconant@ncsu.edu.; Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA. gconant@ncsu.edu.; Program in Genetics, North Carolina State University, Raleigh, NC, USA. gconant@ncsu.edu.
Jazyk: angličtina
Zdroj: BMC bioinformatics [BMC Bioinformatics] 2023 Apr 27; Vol. 24 (1), pp. 174. Date of Electronic Publication: 2023 Apr 27.
DOI: 10.1186/s12859-023-05298-w
Abstrakt: We describe POInT browse , a web portal that gives access to the orthology inferences made for polyploid genomes with POInT, the Polyploidy Orthology Inference Tool. Ancient, or paleo-, polyploidy events are widely distributed across the eukaryotic phylogeny, and the combination of duplicated and lost duplicated genes that these polyploidies produce can confound the identification of orthologous genes between genomes. POInT uses conserved synteny and phylogenetic models to infer orthologous genes between genomes with a shared polyploidy. It also gives confidence estimates for those orthology inferences. POInT browse gives both graphical and query-based access to these inferences from 12 different polyploidy events, allowing users to visualize genomic regions produced by polyploidies and perform batch queries for each polyploidy event, downloading genes trees and coding sequences for orthologous genes meeting user-specified criteria. POInT browse and the associated data are online at https://wgd.statgen.ncsu.edu .
(© 2023. The Author(s).)
Databáze: MEDLINE
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